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Custom PNA Synthesis & Advanced PNA Manufacturing

Bio-Synthesis manufactures standard and advanced peptide nucleic acid (PNA) constructs, including bis-PNA triplex-forming architectures, custom gamma-PNA, PNA–peptide conjugates, fluorescent probes, and multifunctional PNA modifications. Integrated synthesis, conjugation, HPLC purification, and mass spectrometry QC support customer-specified research constructs.

20+ Years of PNA Experience Bis-PNA & Triplex PNA γ-PNA PNA–Peptide Conjugates Fluorescent PNA Probes HPLC / MS QC
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PNA Synthesis Experience Overview Capabilities PNA vs DNA Services Specs Publications FAQ Contact
Why Bio-Synthesis

Over 20 Years of Custom PNA Synthesis Experience

An experienced manufacturing partner helps turn a PNA sequence into a well-defined research reagent. Bio-Synthesis brings together PNA synthesis, custom peptide manufacturing, and conjugation expertise to support projects from initial probe preparation through repeat orders and larger quantities.

Integrated Chemistry Expertise

Coordinate your PNA sequence, peptide partner, label, and linker within one project. Our team reviews the complete construct before selecting a synthesis and purification approach.

Attention to Difficult Sequences

Sequence length, purine-rich regions, aggregation, and hydrophobic labels can affect synthesis and solubility. We review these factors alongside the amount and purity your project requires.

Analytical Documentation

HPLC purity assessment and mass spectrometry identity confirmation help you evaluate the supplied material. Documentation and additional testing requirements are agreed during quotation.

See published research citing Bio-Synthesis PNA synthesis, or discuss your construct with our technical team.

Overview

What Is Peptide Nucleic Acid (PNA)?

Peptide nucleic acid (PNA) is a synthetic nucleic acid analog that recognizes complementary DNA and RNA. In standard PNA, a neutral N-(2-aminoethyl)glycine backbone replaces the sugar-phosphate backbone. This chemistry reduces electrostatic repulsion during hybridization and makes PNA resistant to nuclease degradation. Binding, specificity, and solubility depend on the sequence and assay conditions.

PMO, fully modified TMO, and TMO-DNA/RNA chimera backbone structures

PNA Build

Configured around target sequence, assay format, label position, solubility strategy, conjugation partner, and QC requirements.

Typical Length

5-40 mer; many diagnostic probes use shorter high-affinity designs.

Labeling Options

N-terminus, C-terminus, and internal labels using spacer/linker strategies.

QC Support

mass spectrometry identity confirmation and analytical HPLC; additional testing subject to project review.

Best-Fit Uses

Designed for projects that require stable, short, high-specificity probes with strong DNA/RNA recognition.

PCR Clamping

Wild-type suppression and mutant allele enrichment workflows.

FISH / ISH

Telomere, pathogen, chromosome, and localization probe applications.

Diagnostics

SNP genotyping, mutation detection, capture, pull-down, and probe assays.

Sequence notation: specify PNA sequences from the N-terminus to the C-terminus and identify all terminal groups, labels, and linker positions.

Final quantity: tell us how much purified product you need. Starting synthesis scale and final delivered yield are different specifications.

Explore Our PNA Platform

Advanced PNA Architectures & Specialty Conjugates

Explore custom PNA synthesis beyond conventional linear probes. Bio-Synthesis supports customer-specified recognition architectures, peptide conjugates, specialty linkers, and labeled PNA constructs. Feasibility depends on monomer availability, sequence, and final specifications.

CORE SERVICE

Standard & Modified PNA

Linear PNA probes with custom lengths, terminal groups, fluorescent labels, affinity tags, and solubility-enhancing modifications.

Explore synthesis options →

ADVANCED ARCHITECTURE

Bis-PNA & Triplex-Forming PNA

Two linked PNA recognition domains for homopurine-rich dsDNA targets. AEEA spacers, pseudoisocytosine (J), lysine tails, and biotin modifications can be evaluated.

Explore bis-PNA synthesis →

BACKBONE ENGINEERING

γ-PNA Synthesis

Gamma-substituted PNA architectures for specialized affinity and conformational research. Monomer identity and stereochemistry require feasibility review.

Explore γ-PNA synthesis →

INTEGRATED CONJUGATION

PNA–Peptide Conjugates

Combine PNA recognition with cell-penetrating, targeting, or functional peptides using defined attachment sites and linkers.

Explore peptide–PNA services →

CUSTOM MODIFICATIONS

Complex & Multifunctional PNA

Specialty constructs with PEG/AEEA linkers, biotin, fluorophores, reactive handles, peptide partners, and combined modifications./p>

Explore modification options →

APPLICATION-FOCUSED

PNA FISH & PCR Clamping

High-affinity fluorescent probes and sequence-selective clamps for imaging, mutation detection, and molecular diagnostics.

Explore PNA FISH probes →

PNA vs DNA/RNA

PNA vs DNA and RNA: Backbone, Binding, and Design Considerations

DNA, RNA, and PNA recognize complementary sequences through base pairing, but their backbones affect hybridization, stability, and synthesis. γ-PNA contains substitutions at the gamma position of the PNA backbone; selected designs can improve conformational preorganization or solubility. The benefits depend on the substituent, stereochemistry, sequence, and assay. Custom γ-PNA requests require review of the specified monomers and reagent availability.

Comparison of DNA/RNA, standard PNA, and gamma-modified PNA
Feature DNA / RNA Standard PNA γ-PNA
Backbone Sugar-phosphate backbone Neutral N-(2-aminoethyl)glycine backbone PNA backbone with defined gamma-position substituents
Charge Generally negatively charged Neutral backbone; terminal groups and conjugates can add charge Depends on backbone substituents and attached groups
Target Binding Depends on sequence, duplex type, and conditions Often strong binding to complementary DNA or RNA Selected designs can enhance affinity through preorganization
Mismatch Discrimination Depends on probe design and assay conditions Single-base mismatches can destabilize binding; useful for allele-selective probes Depends on modification, mismatch position, and assay conditions
Nuclease Resistance Unmodified DNA and RNA are susceptible to nucleases Synthetic backbone is highly resistant to nucleases Synthetic backbone retains strong nuclease resistance
Salt Dependence Duplex stability depends on ionic strength Often less salt dependent than DNA/DNA binding Depends on the specific construct and assay
Solubility Depends on sequence, length, and modifications Can be limited by sequence and aggregation Hydrophilic substitutions can improve solubility in selected designs
Synthesis Usually phosphoramidite chemistry Specialized solid-phase synthesis using peptide-type chemistry Modified PNA monomers and specialized synthesis
Research Uses PCR, sequencing, hybridization, and gene regulation PCR clamps, FISH probes, capture, and antisense research Specialized probe and targeting research
Mechanisms of Action

Mechanisms of action of PNA in diagnostics

PNA probes support molecular diagnostics through strong sequence-specific hybridization, mismatch discrimination, polymerase blocking activity, and stable probe-target duplex formation.

PCR Clamp Blocking

PNA clamps hybridize strongly to complementary wild-type DNA sequences and can block polymerase extension during PCR, improving mutation enrichment and SNP discrimination.

Fluorescent Hybridization Detection

Fluorescent PNA probes support FISH and imaging workflows through stable target hybridization, strong mismatch discrimination, and high signal specificity.

Sequence-Specific Targeting

High-affinity PNA duplex formation supports antisense targeting, capture assays, molecular diagnostics, and sequence-selective RNA or DNA recognition workflows.

Applications

Common custom PNA research and diagnostic applications

PNA probes are useful when high binding affinity, mismatch discrimination, nuclease resistance, and compact probe design are important.

PCR Clamping

Suppress wild-type amplification and enrich mutant allele detection in mutation-specific PCR workflows.

SNP & Mutation Detection

High mismatch discrimination for genotyping, rare variant detection, and molecular diagnostic assay development.

FISH / ISH Probes

Fluorescent PNA probes for telomeres, pathogens, chromosomes, transcripts, and localization assays.

Antisense / Antigene Research

Sequence-specific targeting of RNA or DNA for gene regulation and target validation studies.

Capture & Pull-Down

Biotinylated or affinity-tagged PNA probes for target capture and enrichment workflows.

Conjugate Development

Peptide-PNA, dye-PNA, linker-PNA, and solubility-enhanced PNA constructs for specialized assays.

Synthesis Options

Custom PNA synthesis specifications

PNA projects can be configured around probe length, label placement, solubility, purification, analytical requirements, and final application.

Parameter Available Options
Length 5-40 mer; shorter designs are common for high-affinity probes and clamps
Scale Research scale through larger project quantities
Purification HPLC standard; additional purification options by project need
Labels FAM, TAMRA, Cy3, Cy5, biotin, Dabcyl, quencher, and custom labels
Conjugation Peptide, linker, spacer, solubility enhancer, affinity tag, and custom bioconjugates
QC MALDI-TOF or ESI MS identity confirmation and analytical HPLC
Delivery Format Lyophilized or buffered format by request
Modifications & Conjugation

PNA labels, linkers, solubility groups, and conjugates

Bio-Synthesis supports custom PNA designs for detection, capture, uptake, spacing, solubility, and assay-specific performance.

Labels & Functional Handles

detection, capture, and assay readout

PNA probes can be configured with fluorophores, quenchers, affinity tags, reactive handles, and spacer systems.

Fluorescent Dyes
FAM, TAMRA, Cy3, Cy5, ATTO, Alexa Fluor, and other dye options.
Affinity Tags
Biotin, digoxigenin, and custom capture handles.
Reactive Handles
Amine, thiol, azide, alkyne, maleimide, and related coupling groups.

Conjugates & Solubility Design

delivery, spacing, and performance support

PNA properties can be tuned using peptide conjugation, charged residues, spacers, and application-specific linkers.

Peptide-PNA
CPP, targeting peptide, and functional peptide conjugation options.
Spacer Systems
AEEA, PEG, and custom linkers for steric spacing and signal performance.
Solubility Support
Lysine tails, charged residues, and design review for difficult sequences.
Specialized PNA Services

Specialized PNA Services & Connected Capabilities

Explore application-specific PNA services and conjugation workflows. Dedicated service pages cover bis-PNA, γ-PNA, and complex PNA conjugates, alongside existing PNA–peptide and FISH capabilities.

Custom PNA–Peptide Conjugate Synthesis

Combine a sequence-specific PNA with a cell-penetrating peptide, targeting peptide, or other functional peptide for delivery and target-recognition research. Attachment position, peptide sequence, linker chemistry, and solubility are reviewed for the complete construct.

Biological uptake and activity depend on the construct and experimental system; conjugation chemistry is selected around your research requirements.

Explore PNA–peptide conjugation services →

Custom Fluorescent PNA FISH Probes

Order sequence-specific PNA probes for fluorescence in situ hybridization (FISH), including chromosome, telomere, and microbial target studies. Specify the target sequence, dye, label position, and sample format.

For multiplex imaging, share the instrument channels and other fluorophores in your experiment so labeling options can be reviewed.

Explore custom PNA FISH probe synthesis →

For existing product options, view telomere and centromere PNA FISH probes.

Quality & Documentation

PNA Purification, Mass Spectrometry, and Quality Control

Define purity, identity testing, and documentation needs before synthesis. HPLC assesses chromatographic purity, while mass spectrometry compares the observed mass with the expected construct. These measurements characterize the supplied reagent; assay performance is evaluated in your experimental system.

Identity Confirmation

  • MALDI-TOF or ESI mass spectrometry
  • Molecular weight confirmation
  • Lot-linked analytical review

Purity Assessment

  • Analytical HPLC chromatogram
  • Purity reporting
  • Additional testing by request

Documentation

  • Certificate of Analysis
  • Optional Tm or assay support
  • Project-specific records available
Planning Your Order

PNA Sequence, Solubility, and Conjugate Design Considerations

Selected peer-reviewed publications referencing peptide nucleic acid technologies and Bio-Synthesis synthesis support for diagnostic, antisense, and molecular targeting applications.

Define Sequence and Orientation

Provide the PNA sequence in N-to-C orientation, the complementary target, and the application. For clamps or allele-selective probes, identify the variant and surrounding sequence. For FISH, specify the organism and target region.

Specify Labels and Linkers

Identify terminal groups, dye or biotin positions, spacer structure, and peptide sequence. AEEA, PEG-based spacers, and charged residues may help with spacing or solubility, depending on the design.

Order the Final Amount You Need

Specify the required purified yield in nmol, µmol, or mg, along with purity and delivery format. Conjugation and purification affect recovery, so the initial synthesis scale is selected after review of the final requirements.

If you need material in solution, include the requested buffer, concentration, and total volume. Sequence-dependent solubility should be reviewed before confirming a formulation.

Frequently asked questions about custom PNA synthesis

FAQ

Can Bio-Synthesis manufacture PNA–peptide conjugates?
Yes. Bio-Synthesis supports custom PNA–peptide conjugates, including cell-penetrating and targeting peptide constructs. The PNA sequence, peptide sequence, attachment sites, linker, final yield, and purification requirements are reviewed before quotation.
Can I order fluorescent PNA FISH probes?
Yes. Provide the PNA sequence or target region, organism, fluorophore, label position, and final amount. For multiplex FISH, include the instrument channels and other dyes in use. Dye availability and conjugation compatibility are reviewed for each project.
What PNA lengths and modifications are available?
The listed synthesis range is 5–40 bases, subject to sequence and modification review. Fluorophores, biotin, spacers, reactive handles, and peptide conjugates can be considered. Longer, purine-rich, or heavily modified constructs may need additional synthesis and solubility evaluation.
Do you offer γ-PNA synthesis?
Custom γ-PNA requests are reviewed against the specified gamma-position substituent, stereochemistry, monomer availability, and sequence. Please provide the requested structure or a literature reference so the team can evaluate feasibility, cost, and lead time.
What is peptide nucleic acid (PNA)?
PNA is a synthetic nucleic acid analog with a peptide-like backbone. Standard PNA contains N-(2-aminoethyl)glycine units instead of a sugar-phosphate backbone and binds complementary DNA or RNA through base pairing.
How is PNA synthesis different from DNA or RNA synthesis?
PNA uses specialized solid-phase synthesis with peptide-type coupling chemistry. DNA and RNA are typically synthesized using phosphoramidite chemistry. Combining these materials requires a compatible linker and a defined conjugation strategy.
What information is needed for a PNA synthesis quote?
 Provide the N-to-C PNA sequence, target and application, terminal groups, modifications or peptide partner, required final purified quantity, purity, delivery format, and analytical documentation. A requested delivery date also helps with project planning.
How are PNA purity and identity assessed?
 Analytical HPLC is used to assess chromatographic purity, and MALDI-TOF or ESI mass spectrometry is used for identity confirmation. Specify the purity requirement and documentation needed during quotation.
Can PNA discriminate a single-base mismatch?
 PNA can be useful for single-base discrimination because mismatches can reduce duplex stability. Discrimination depends on probe sequence, mismatch position, temperature, and buffer; the assay conditions need experimental optimization.
Why can PNA solubility be challenging?
 Solubility depends on sequence, length, aggregation, and attached labels or peptides. Charged residues, hydrophilic spacers, or selected backbone modifications may help, but changes should be reviewed for compatibility with the intended assay.
Can Bio-Synthesis synthesize bis-PNA for triplex invasion?
Custom bis-PNA synthesis can be evaluated for customer-specified Watson–Crick and Hoogsteen recognition arms, flexible AEEA linkers, pseudoisocytosine (J) substitutions, and terminal labels. Efficient invasion of intact dsDNA depends on target sequence, topology, and assay conditions and is not guaranteed.
Can bis-PNA include biotin-PEG4 or multiple AEEA spacers?
Terminal biotin-PEG4 and AEEA spacer configurations can be reviewed for synthesis feasibility. The optimal spacer length and accessibility for streptavidin or DNA binding require experimental validation.
More FAQsAll FAQs
Contact & Quote Request

Request a Custom PNA Synthesis Quote

Send your PNA sequence in N-to-C orientation, target and application, terminal groups, labels or peptide partner, required final purified yield, purity, and delivery format. Our technical team will review the construct and recommend a synthesis, conjugation, and purification approach for quotation.
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Why Choose Bio-Synthesis

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Greetings, Researchers,

Please be advised that any information, guidelines, write-ups, and oral/video/graphic content on our website are intended solely as general guidelines.

It is the researcher's sole responsibility to conduct thorough research on the design of products intended for their experiments before submitting
their designs to Biosynthesis for production feasibility review.

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